500 lines
20 KiB
Python
500 lines
20 KiB
Python
 
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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get_WoLF_PSORT_out_fixed.py
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修复版 - 根据实际HTML结构自动化从WoLF PSORT网站获取预测结果
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使用方法: python get_WoLF_PSORT_out_fixed.py --input <fasta文件> --output <结果文件>
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"""
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import argparse
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import time
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import os
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import re
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import sys
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import shutil
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from selenium import webdriver
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from selenium.webdriver.common.by import By
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from selenium.webdriver.firefox.options import Options
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from selenium.webdriver.firefox.service import Service
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from selenium.webdriver.support.ui import WebDriverWait
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from selenium.webdriver.support import expected_conditions as EC
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def get_WoLF_PSORT_out_fixed(arg1, arg2):
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"""修复版 - 使用正确的元素定位从WoLF PSORT获取结果"""
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# 1. 读取FASTA文件
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fa_dict = {}
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with open(arg1, "rt") as fr:
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current_id = ""
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for line in fr:
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line = line.strip()
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if not line:
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continue
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if line.startswith(">"):
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current_id = line[1:].split()[0] if " " in line[1:] else line[1:]
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fa_dict[current_id] = ""
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else:
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fa_dict[current_id] += line.replace(" ", "")
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print(f"成功读取 {len(fa_dict)} 条蛋白质序列")
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print(f"示例ID: {list(fa_dict.keys())[:3]}")
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# 2. 配置Firefox选项
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options = Options()
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options.set_preference("dom.webdriver.enabled", False)
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options.set_preference("useAutomationExtension", False)
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options.add_argument("-headless")
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# 3. 初始化Firefox驱动
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geckodriver_path = shutil.which("geckodriver") or "/usr/local/bin/geckodriver"
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print(f"使用geckodriver路径: {geckodriver_path}")
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try:
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service = Service(executable_path=geckodriver_path)
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driver = webdriver.Firefox(service=service, options=options)
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print("Firefox驱动初始化成功")
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except Exception as e:
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print(f"驱动初始化失败: {e}")
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print("请检查: 1) geckodriver路径是否正确 2) Firefox是否已安装")
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sys.exit(2)
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try:
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# 访问目标网站
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print("访问WoLF PSORT网站...")
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driver.get("https://wolfpsort.hgc.jp/")
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print("成功访问WoLF PSORT网站")
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# 等待页面加载完成
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wait = WebDriverWait(driver, 30)
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time.sleep(2) # 额外等待确保页面完全加载
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# ===== 第一步：选择生物体类型为 Plant =====
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print("选择生物体类型: Plant...")
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try:
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# 根据debug.html，正确的选择器是：name="organism_type" value="plant"
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plant_radio = wait.until(
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EC.presence_of_element_located((By.CSS_SELECTOR, 'input[name="organism_type"][value="plant"]'))
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)
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# 先检查是否已选中，未选中则点击
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if not plant_radio.is_selected():
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print(" 点击Plant单选按钮...")
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plant_radio.click()
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# 等待一下让JavaScript激活提交按钮
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time.sleep(1)
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else:
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print(" Plant已默认选中")
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print(" ✓ 已选择Plant")
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except Exception as e:
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print(f" ✗ 选择Plant失败: {e}")
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# 尝试备用定位方式
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try:
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radios = driver.find_elements(By.NAME, "organism_type")
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for radio in radios:
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if radio.get_attribute("value") == "plant":
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if not radio.is_selected():
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radio.click()
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time.sleep(1)
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print(" ✓ 已选择Plant（备用方式）")
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break
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except:
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print(" ⚠ 无法选择Plant，可能影响后续提交")
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# ===== 第二步：选择输入方式为 From File =====
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print("选择输入方式: From File...")
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try:
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# 根据debug.html，正确的选择器是：name="input_type" value="file"
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time.sleep(1)
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# 查找"From File"的radio按钮
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file_radio = wait.until(
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EC.presence_of_element_located((By.CSS_SELECTOR, 'input[name="input_type"][value="file"]'))
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)
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if not file_radio.is_selected():
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file_radio.click()
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print(" ✓ 已选择From File")
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else:
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print(" ✓ From File已默认选中")
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except Exception as e:
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print(f" 选择From File时出错: {e}")
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try:
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# 尝试通过XPath定位所有input_type
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radios = driver.find_elements(By.NAME, "input_type")
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for radio in radios:
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if radio.get_attribute("value") == "file":
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if not radio.is_selected():
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radio.click()
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print(" ✓ 已选择From File（备用方式）")
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break
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except:
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print(" ⚠ 无法选择From File")
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# ===== 第三步：上传FASTA文件 =====
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print(f"上传FASTA文件: {arg1}...")
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try:
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time.sleep(1)
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# 根据debug.html，正确的选择器是：name="sequence_file" type="file"
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file_input = wait.until(
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EC.presence_of_element_located((By.CSS_SELECTOR, 'input[name="sequence_file"][type="file"]'))
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)
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# 确保文件路径是绝对路径
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fasta_path = os.path.abspath(arg1)
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print(f" 文件绝对路径: {fasta_path}")
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if not os.path.exists(fasta_path):
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print(f" ✗ 文件不存在: {fasta_path}")
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return
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# 上传文件
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file_input.send_keys(fasta_path)
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print(" ✓ 已上传文件")
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# 确认文件已上传
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time.sleep(1)
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except Exception as e:
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print(f" ✗ 文件上传失败: {e}")
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# 尝试其他可能的定位
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try:
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file_inputs = driver.find_elements(By.TAG_NAME, "input")
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for input_elem in file_inputs:
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if input_elem.get_attribute("type") == "file":
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fasta_path = os.path.abspath(arg1)
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input_elem.send_keys(fasta_path)
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print(" ✓ 已上传文件（备用方式）")
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break
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except Exception as e2:
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print(f" ✗ 备用上传方式也失败: {e2}")
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return
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# ===== 第四步：点击提交按钮 =====
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print("点击提交按钮...")
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try:
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time.sleep(1)
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# 根据debug.html，提交按钮的name是"submit_sequence"
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# 注意：这个按钮在未选择生物体类型时是禁用的
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submit_btn = wait.until(
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EC.element_to_be_clickable((By.CSS_SELECTOR, 'input[name="submit_sequence"][type="submit"]'))
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)
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# 滚动到按钮位置
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driver.execute_script("arguments[0].scrollIntoView(true);", submit_btn)
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time.sleep(0.5)
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# 点击提交按钮
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submit_btn.click()
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print(" ✓ 已提交，等待处理结果...")
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except Exception as e:
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print(f" ✗ 提交失败（可能按钮仍被禁用）: {e}")
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# 尝试通过JavaScript直接提交表单
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try:
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driver.execute_script("document.forms[0].submit();")
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print(" ✓ 已通过JavaScript提交表单")
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except Exception as e2:
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print(f" ✗ JavaScript提交也失败: {e2}")
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return
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# ===== 第五步：等待处理完成 =====
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print("等待服务器处理...")
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# 设置总等待时间
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total_wait_time = 300 # 最长等待5分钟
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start_time = time.time()
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result_found = False
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result_page_source = ""
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while time.time() - start_time < total_wait_time:
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elapsed = int(time.time() - start_time)
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# 每15秒报告一次状态
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if elapsed > 0 and elapsed % 15 == 0:
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print(f" 已等待 {elapsed} 秒...")
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try:
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# 获取当前页面源代码
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if elapsed % 8 == 0: # 每8秒检查一次
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result_page_source = driver.page_source
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# 检查是否出现结果（根据你的示例格式）
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if "FtPinG" in result_page_source and "details" in result_page_source:
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print(f" ✓ 检测到结果内容！总耗时: {elapsed}秒")
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result_found = True
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break
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# 检查是否出现错误
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if "error" in result_page_source.lower():
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print(" ✗ 检测到错误信息")
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# 保存错误页面
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with open("wolfpsort_error.html", "w", encoding="utf-8") as f:
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f.write(result_page_source)
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print(" 错误页面已保存到: wolfpsort_error.html")
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break
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# 检查URL是否包含results
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current_url = driver.current_url
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if "results/" in current_url:
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print(f" ✓ 已跳转到结果页面，总耗时: {elapsed}秒")
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result_found = True
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time.sleep(3) # 等待结果完全加载
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break
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# 检查是否还在处理中（可能出现的提示文本）
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if "processing" in result_page_source.lower() or "please wait" in result_page_source.lower():
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pass # 正常，继续等待
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except Exception as e:
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# 页面可能还在跳转中，忽略特定错误
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if "document.documentElement is null" not in str(e):
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print(f" 检查页面时出错: {e}")
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time.sleep(3) # 每次循环等待3秒
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# 检查是否超时
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if not result_found:
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if time.time() - start_time >= total_wait_time:
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print(f" ⚠ 等待超时（{total_wait_time}秒）")
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else:
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print(" ⚠ 未检测到结果内容")
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# 尝试获取最后一次的页面内容
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try:
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result_page_source = driver.page_source
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except:
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print(" ✗ 无法获取页面源代码")
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return
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# ===== 第六步：解析结果（关键修复部分）=====
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print("解析结果页面...")
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# 保存原始页面用于调试
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debug_file = arg2.replace(".txt", "_debug.html")
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try:
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with open(debug_file, "w", encoding="utf-8") as f:
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f.write(result_page_source)
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print(f" ✓ 原始页面已保存到: {debug_file}")
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except Exception as e:
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print(f" ✗ 保存调试文件失败: {e}")
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# 解析结果 - 根据实际HTML格式修复
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results = {}
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# 主解析模式：匹配HTML中的格式 <protein_id> <a href="...">details</a> <location_info>
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# 示例: FtPinG0009145900.01.T01 <a href="...">details</a> nucl: 5, vacu: 4, ...
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primary_pattern = re.compile(r'([A-Za-z0-9_.\-]+)\s*<a\s+[^>]*>details</a>\s*([^<]+)')
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matches = primary_pattern.findall(result_page_source)
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if matches:
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print(f" 找到 {len(matches)} 条预测结果（主模式）")
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for protein_id, location in matches:
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protein_id = protein_id.strip()
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location = location.strip()
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results[protein_id] = location
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if len(results) <= 5: # 只显示前5条
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print(f" {protein_id}: {location[:60]}...")
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else:
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# 备用模式1：匹配可能的变体格式
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backup_pattern1 = re.compile(r'>?([A-Za-z0-9_.\-]+).*?details.*?>([^<]+)')
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matches = backup_pattern1.findall(result_page_source, re.IGNORECASE | re.DOTALL)
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if matches:
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print(f" 找到 {len(matches)} 条预测结果（备用模式1）")
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for protein_id, location in matches:
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protein_id = re.sub(r'^>', '', protein_id).strip() # 移除可能的前导'>'
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location = location.strip()
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# 清理可能的多余字符
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location = re.sub(r'^\s*:\s*', '', location) # 移除开头的冒号
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results[protein_id] = location
|
|||
|
|
if len(results) <= 5:
|
|||
|
|
print(f" {protein_id}: {location[:60]}...")
|
|||
|
|
else:
|
|||
|
|
# 备用模式2：逐行解析（最保守的方法）
|
|||
|
|
print(" 使用逐行解析模式...")
|
|||
|
|
lines = result_page_source.split('\n')
|
|||
|
|
for line in lines:
|
|||
|
|
line = line.strip()
|
|||
|
|
# 查找包含"details"和定位信息（如nucl:, chlo:, cyto:）的行
|
|||
|
|
if 'details' in line.lower() and any(marker in line for marker in ['nucl:', 'chlo:', 'cyto:', 'vacu:', 'plas:', 'mito:']):
|
|||
|
|
# 尝试分割ID和结果
|
|||
|
|
if 'details' in line:
|
|||
|
|
parts = line.split('details', 1)
|
|||
|
|
if len(parts) == 2:
|
|||
|
|
protein_id = parts[0].strip()
|
|||
|
|
location = parts[1].strip()
|
|||
|
|
|
|||
|
|
# 清理HTML标签
|
|||
|
|
protein_id = re.sub(r'<[^>]+>', '', protein_id)
|
|||
|
|
location = re.sub(r'<[^>]+>', '', location)
|
|||
|
|
|
|||
|
|
# 移除可能的"<a>"标签
|
|||
|
|
location = re.sub(r'^[^a-zA-Z]*', '', location)
|
|||
|
|
|
|||
|
|
if protein_id and location:
|
|||
|
|
results[protein_id] = location
|
|||
|
|
print(f" {protein_id}: {location[:60]}...")
|
|||
|
|
|
|||
|
|
# 如果没有找到任何结果，保存原始页面以便手动检查
|
|||
|
|
if not results:
|
|||
|
|
print(" ✗ 无法解析任何结果")
|
|||
|
|
raw_output = arg2.replace(".txt", "_raw_output.txt")
|
|||
|
|
with open(raw_output, "w", encoding="utf-8") as f:
|
|||
|
|
f.write(result_page_source)
|
|||
|
|
print(f" 原始结果已保存到: {raw_output}")
|
|||
|
|
|
|||
|
|
# ===== 第七步：保存结果 =====
|
|||
|
|
print(f"\n保存结果到: {arg2}")
|
|||
|
|
|
|||
|
|
# 写入结果文件
|
|||
|
|
with open(arg2, "w") as fw:
|
|||
|
|
fw.write("Protein_ID\tWoLF_PSORT_Prediction\n")
|
|||
|
|
|
|||
|
|
matched_count = 0
|
|||
|
|
unmatched_count = 0
|
|||
|
|
matched_ids = []
|
|||
|
|
|
|||
|
|
for original_id in fa_dict.keys():
|
|||
|
|
# 尝试多种匹配策略
|
|||
|
|
matched = False
|
|||
|
|
|
|||
|
|
# 策略1: 精确匹配
|
|||
|
|
if original_id in results:
|
|||
|
|
fw.write(f"{original_id}\t{results[original_id]}\n")
|
|||
|
|
matched_count += 1
|
|||
|
|
matched_ids.append(original_id)
|
|||
|
|
matched = True
|
|||
|
|
else:
|
|||
|
|
# 策略2: 部分匹配（包含关系）
|
|||
|
|
for result_id in results.keys():
|
|||
|
|
# 如果原始ID包含在结果ID中，或结果ID包含在原始ID中
|
|||
|
|
if (original_id in result_id) or (result_id in original_id):
|
|||
|
|
fw.write(f"{original_id}\t{results[result_id]}\n")
|
|||
|
|
matched_count += 1
|
|||
|
|
matched_ids.append(original_id)
|
|||
|
|
matched = True
|
|||
|
|
break
|
|||
|
|
|
|||
|
|
# 策略3: 简化匹配（去除版本号等后缀）
|
|||
|
|
if not matched:
|
|||
|
|
# 尝试移除点后面的部分（如.01.T01）
|
|||
|
|
simple_id = original_id.split('.')[0] if '.' in original_id else original_id
|
|||
|
|
for result_id in results.keys():
|
|||
|
|
simple_result_id = result_id.split('.')[0] if '.' in result_id else result_id
|
|||
|
|
if simple_id == simple_result_id:
|
|||
|
|
fw.write(f"{original_id}\t{results[result_id]}\n")
|
|||
|
|
matched_count += 1
|
|||
|
|
matched_ids.append(original_id)
|
|||
|
|
matched = True
|
|||
|
|
break
|
|||
|
|
|
|||
|
|
if not matched:
|
|||
|
|
fw.write(f"{original_id}\tNot Found\n")
|
|||
|
|
unmatched_count += 1
|
|||
|
|
print(f" ⚠ 未找到匹配: {original_id}")
|
|||
|
|
|
|||
|
|
# 输出统计信息
|
|||
|
|
print("\n" + "="*60)
|
|||
|
|
print("处理完成统计:")
|
|||
|
|
print(f" 总序列数: {len(fa_dict)}")
|
|||
|
|
print(f" 结果页面找到: {len(results)} 条预测")
|
|||
|
|
print(f" 成功匹配: {matched_count}")
|
|||
|
|
print(f" 未匹配: {unmatched_count}")
|
|||
|
|
if len(fa_dict) > 0:
|
|||
|
|
success_rate = (matched_count/len(fa_dict))*100
|
|||
|
|
print(f" 匹配率: {success_rate:.1f}%")
|
|||
|
|
if success_rate < 100:
|
|||
|
|
print(f" 未匹配的序列: {unmatched_count} 条")
|
|||
|
|
print("="*60)
|
|||
|
|
|
|||
|
|
# 显示部分结果示例
|
|||
|
|
if matched_count > 0:
|
|||
|
|
print("\n结果示例（前5条）:")
|
|||
|
|
count = 0
|
|||
|
|
with open(arg2, "r") as fr:
|
|||
|
|
for line in fr.readlines()[1:6]:
|
|||
|
|
print(f" {line.strip()}")
|
|||
|
|
count += 1
|
|||
|
|
if count >= 5:
|
|||
|
|
break
|
|||
|
|
|
|||
|
|
print(f"\n完成！结果已保存到: {arg2}")
|
|||
|
|
if os.path.exists(debug_file):
|
|||
|
|
print(f"调试页面已保存到: {debug_file}")
|
|||
|
|
|
|||
|
|
# 如果匹配率不高，提示用户检查
|
|||
|
|
if len(fa_dict) > 0 and (matched_count/len(fa_dict)) < 0.9:
|
|||
|
|
print("\n⚠ 注意：匹配率较低，建议检查以下内容：")
|
|||
|
|
print(" 1. 检查输入FASTA文件中的ID格式")
|
|||
|
|
print(" 2. 检查结果页面中的ID格式")
|
|||
|
|
print(f" 3. 查看调试文件: {debug_file}")
|
|||
|
|
|
|||
|
|
except Exception as e:
|
|||
|
|
print(f"\n主流程出错: {e}")
|
|||
|
|
import traceback
|
|||
|
|
traceback.print_exc()
|
|||
|
|
finally:
|
|||
|
|
# 确保浏览器被关闭
|
|||
|
|
try:
|
|||
|
|
driver.quit()
|
|||
|
|
print("\n浏览器已关闭")
|
|||
|
|
except:
|
|||
|
|
pass
|
|||
|
|
|
|||
|
|
|
|||
|
|
def main():
|
|||
|
|
"""主函数"""
|
|||
|
|
parser = argparse.ArgumentParser(
|
|||
|
|
description="修复版 - 自动从WoLF PSORT网站获取蛋白质亚细胞定位预测结果",
|
|||
|
|
formatter_class=argparse.RawDescriptionHelpFormatter,
|
|||
|
|
epilog="""
|
|||
|
|
使用示例:
|
|||
|
|
python %(prog)s --input ../Ft.SPL.pep.fasta --output WoLF_PSORT_out.txt
|
|||
|
|
|
|||
|
|
修复内容:
|
|||
|
|
1. 修正了解析逻辑，使用三层匹配策略确保高匹配率
|
|||
|
|
2. 增强错误处理和调试信息
|
|||
|
|
3. 优化等待机制和结果检测
|
|||
|
|
"""
|
|||
|
|
)
|
|||
|
|
|
|||
|
|
parser.add_argument(
|
|||
|
|
"--input",
|
|||
|
|
required=True,
|
|||
|
|
help="输入FASTA文件路径（包含蛋白质序列）"
|
|||
|
|
)
|
|||
|
|
parser.add_argument(
|
|||
|
|
"--output",
|
|||
|
|
required=True,
|
|||
|
|
help="输出文件路径（结果将写入）"
|
|||
|
|
)
|
|||
|
|
|
|||
|
|
args = parser.parse_args()
|
|||
|
|
|
|||
|
|
# 验证输入文件
|
|||
|
|
if not os.path.exists(args.input):
|
|||
|
|
print(f"错误: 输入文件 '{args.input}' 不存在")
|
|||
|
|
sys.exit(1)
|
|||
|
|
|
|||
|
|
# 显示启动信息
|
|||
|
|
print("=" * 60)
|
|||
|
|
print("WoLF PSORT 亚细胞定位自动化预测（修复版）")
|
|||
|
|
print(f"输入文件: {args.input}")
|
|||
|
|
print(f"输出文件: {args.output}")
|
|||
|
|
print("=" * 60)
|
|||
|
|
|
|||
|
|
# 运行主函数
|
|||
|
|
get_WoLF_PSORT_out_fixed(args.input, args.output)
|
|||
|
|
|
|||
|
|
|
|||
|
|
if __name__ == "__main__":
|
|||
|
|
main()
|